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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ), 'gf_id' => 'HOM05D001310', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001310' ), 'data_identifier' => 'HOM05D001310', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001310', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '480', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p40480' => 'bna', 'A05p31840' => 'bna', 'A06p04360' => 'bna', 'A09p65640' => 'bna', 'A10p27860' => 'bna', 'Aa31LG3G17590' => 'aar', 'Aa31LG8G4830' => 'aar', 'Aa31sc136G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2643' => 'aag', 'Actinidia13000' => 'ach', 'Actinidia13001' => 'ach', 'Actinidia13183' => 'ach', 'Actinidia18896' => 'ach', 'Actinidia18897' => 'ach', 'Actinidia19796' => 'ach', 'Actinidia24639' => 'ach', 'Actinidia24969' => 'ach', 'Actinidia24970' => 'ach', 'Actinidia28053' => 'ach', 'Actinidia28137' => 'ach', 'Actinidia35128' => 'ach', 'Ah.01g022280' => 'amhyb', 'Ah.01g022290' => 'amhyb', 'Ah.06g189220' => 'amhyb', 'Ah.10g032670' => 'amhyb', 'AL1G19410' => 'aly', 'AL3G31130' => 'aly', 'AL6G19810' => 'aly', 'Aqoxy2G03296' => 'aox', 'Aqoxy3G00064' => 'aox', 'Aqoxy6G00773' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5JS7Y0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60IM8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6LU9QT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DEN2HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DWV9W6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ETG9TD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2WU28' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LBLS7P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LPMM03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QD3ZBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QR2JGW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UEZ3ZF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WS4LBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YX4B4M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZLV2ZH' => 'arhy', 'AT1G08980' => 'ath', 'AT3G17970' => 'ath', 'AT5G09420' => 'ath', 'ATR0564G362' => 'atr', 'ATR0626G200' => 'atr', 'ATR0782G125' => 'atr', 'ATR0782G133' => 'atr', 'Atru.chr2.445' => 'acertr', 'Atru.chr6.1140' => 'acertr', 'Atru.chr9.1733' => 'acertr', 'AUR62000842' => 'cqu', 'AUR62005131' => 'cqu', 'AUR62010143' => 'cqu', 'AUR62013138' => 'cqu', 'AUR62025790' => 'cqu', 'AUR62042937' => 'cqu', 'BcaB01g02648' => 'bca', 'BcaB01g02649' => 'bca', 'BcaB04g18975' => 'bca', 'BcaB06g25863' => 'bca', 'BcaB07g33744' => 'bca', 'BcaB08g36561' => 'bca', 'BcaB08g37206' => 'bca', 'BcaB08g37207' => 'bca', 'BcaC01g03719' => 'bca', 'BcaC05g28730' => 'bca', 'BcaC07g41912' => 'bca', 'BcaC08g43058' => 'bca', 'BolC3t17222H' => 'bol', 'BolC5t33567H' => 'bol', 'BolC6t35435H' => 'bol', 'BolC8t52500H' => 'bol', 'BolC9t59555H' => 'bol', 'BraA03t13206Z' => 'bra', 'BraA05t22016Z' => 'bra', 'BraA06t23640Z' => 'bra', 'BraA09t41908Z' => 'bra', 'BraA10t44835Z' => 'bra', 'C03p49320' => 'bna', 'C05p48330' => 'bna', 'C06p03170' => 'bna', 'C08p49720' => 'bna', 'C09p67960' => 'bna', 'CAN.G1.39' => 'can', 'CAN.G509.7' => 'can', 'CAN.G843.55' => 'can', 'CANSAT54G0385' => 'cansat', 'CANSAT80G2848' => 'cansat', 'CARHR008880' => 'chi', 'CARHR093290' => 'chi', 'CARHR203980' => 'chi', 'CARHR292250' => 'chi', 'Carub.0001s0829' => 'cru', 'Carub.0001s0830' => 'cru', 'Carub.0003s1769' => 'cru', 'Carub.0006s0797' => 'cru', 'Ca_10104_v3' => 'car', 'Ca_17191_v3' => 'car', 'Ca_18358_v3' => 'car', 'CBR_g36926' => 'cbr', 'Cc00_g15590' => 'ccan', 'Cc02_g21470' => 'ccan', 'Cc04_g06250' => 'ccan', 'CDE05G1658' => 'cde', 'CDE05G3325' => 'cde', 'CDE10G0845' => 'cde', 'CDE11G0307' => 'cde', 'Cfa005584' => 'cfa', 'Cfa006573' => 'cfa', 'Cfa006574' => 'cfa', 'Cfa006575' => 'cfa', 'Cfa015126' => 'cfa', 'Cfa021204' => 'cfa', 'Cfa024115' => 'cfa', 'Cfa026599' => 'cfa', 'Ciclev10001213m.g' => 'ccl', 'Ciclev10001239m.g' => 'ccl', 'Ciclev10007714m.g' => 'ccl', 'Ciclev10028606m.g' => 'ccl', 'CiPaw.05G034800' => 'cil', 'CiPaw.07G016200' => 'cil', 'CiPaw.07G016400' => 'cil', 'CiPaw.15G143400' => 'cil', 'CiPaw.16G093500' => 'cil', 'ClCG00G001670' => 'cla', 'ClCG03G016900' => 'cla', 'ClCG06G014290' => 'cla', 'ClCG06G014300' => 'cla', 'ClCG09G015490' => 'cla', 'COL.COLO4_04375' => 'col', 'COL.COLO4_08574' => 'col', 'COL.COLO4_13489' => 'col', 'COL.COLO4_13495' => 'col', 'COL.COLO4_13496' => 'col', 'COL.COLO4_20745' => 'col', 'Cpa.g.sc3.396' => 'cpa', 'Cpa.g.sc42.43' => 'cpa', 'Cpa.g.sc42.44' => 'cpa', 'Cpa.g.sc48.34' => 'cpa', 'Cre02.g114850' => 'cre', 'Cre08.g360100' => 'cre', 'Cre11.g467630' => 'cre', 'CsaV3_1G004380' => 'csa', 'CsaV3_1G039020' => 'csa', 'CsaV3_1G039030' => 'csa', 'CsaV3_7G006560' => 'csa', 'CSS0011156' => 'camsi', 'CSS0018609' => 'camsi', 'CSS0019715' => 'camsi', 'CSS0021078' => 'camsi', 'CSS0022622' => 'camsi', 'CSS0036070' => 'camsi', 'CSS0040216' => 'camsi', 'CSS0046230' => 'camsi', 'DCAR_014505' => 'dca', 'DCAR_017063' => 'dca', 'DCAR_021862' => 'dca', 'DCAR_029426' => 'dca', 'Dinv04126' => 'din', 'Dinv04127' => 'din', 'Dinv04131' => 'din', 'Dinv09029' => 'din', 'Dinv24185' => 'din', 'Dinv40274' => 'din', 'Duzib052G0331' => 'dzi', 'Duzib052G0493' => 'dzi', 'Duzib068G0977' => 'dzi', 'Duzib106G0949' => 'dzi', 'Duzib132G0694' => 'dzi', 'Duzib177G0013' => 'dzi', 'Duzib177G0593' => 'dzi', 'Duzib177G0831' => 'dzi', 'Duzib177G1171' => 'dzi', 'Duzib205G1371' => 'dzi', 'ECA233G3392' => 'eca', 'ECA238G4171' => 'eca', 'ECA240G0103' => 'eca', 'EL10Ac4g09339' => 'bvu', 'EL10Ac5g11565' => 'bvu', 'EL10Ac9g21487' => 'bvu', 'Eucgr.B01994' => 'egr', 'Eucgr.B01996' => 'egr', 'Eucgr.I02661' => 'egr', 'Eucgr.K02274' => 'egr', 'Eucgr.L03224' => 'egr', 'FAN02G1114' => 'fan', 'FAN04G0115' => 'fan', 'FAN05G0213' => 'fan', 'FAN05G4155' => 'fan', 'FAN08G1056' => 'fan', 'FAN09G2049' => 'fan', 'FAN13G2361' => 'fan', 'FAN14G5181' => 'fan', 'FAN14G5649' => 'fan', 'FAN18G0790' => 'fan', 'FAN18G2658' => 'fan', 'FvH4_5g17380' => 'fve', 'FvH4_6g05640' => 'fve', 'Glyma.05G116700' => 'gma', 'Glyma.05G246300' => 'gma', 'Glyma.08G054300' => 'gma', 'Glyma.08G178700' => 'gma', 'Glyma.08G197900' => 'gma', 'Glyma.10G155400' => 'gma', 'Glyma.15G053800' => 'gma', 'Glyma.20G232900' => 'gma', 'Gohir.A03G174600' => 'ghi', 'Gohir.A11G003100' => 'ghi', 'Gohir.A11G264000' => 'ghi', 'Gohir.A11G264133' => 'ghi', 'Gohir.A12G015200' => 'ghi', 'Gohir.D02G197800' => 'ghi', 'Gohir.D08G154580' => 'ghi', 'Gohir.D11G002700' => 'ghi', 'Gohir.D11G274100' => 'ghi', 'Gohir.D11G274200' => 'ghi', 'Gohir.D12G015600' => 'ghi', 'Gorai.005G221100' => 'gra', 'Gorai.007G003700' => 'gra', 'Gorai.007G295700' => 'gra', 'Gorai.007G295900' => 'gra', 'Gorai.008G015700' => 'gra', 'GSVIVG01000036001' => 'vvi', 'GSVIVG01008433001' => 'vvi', 'GSVIVG01038788001' => 'vvi', 'HanXRQChr03g0067581' => 'han', 'HanXRQChr05g0142631' => 'han', 'HanXRQChr05g0142641' => 'han', 'HanXRQChr13g0420761' => 'han', 'HanXRQChr14g0446451' => 'han', 'Haze_04208' => 'cav', 'Haze_10723' => 'cav', 'Haze_18852' => 'cav', 'Haze_18854' => 'cav', 'Hma1.2p1_0522F.1_g171690' => 'hma', 'Hma1.2p1_0669F.1_g200140' => 'hma', 'Hma1.2p1_1362F.1_g278280' => 'hma', 'HPP92_004126' => 'vpl', 'HPP92_013662' => 'vpl', 'HPP92_013681' => 'vpl', 'HPP92_016785' => 'vpl', 'HPP92_016787' => 'vpl', 'Hund00067' => 'sun', 'Hund02255' => 'sun', 'Hund21815' => 'sun', 'Lalb_Chr05g0217541' => 'lal', 'Lalb_Chr05g0221661' => 'lal', 'Lalb_Chr15g0090421' => 'lal', 'Lalb_Chr15g0090431' => 'lal', 'Lalb_Chr16g0387011' => 'lal', 'Lalb_Chr21g0310741' => 'lal', 'Lj2g0012825' => 'lja', 'Lj2g0027653' => 'lja', 'Lj4g0007471' => 'lja', 'Lj4g0014215' => 'lja', 'Lj5A239G80' => 'lonja', 'Lj5A552T18' => 'lonja', 'Lj5A559T31' => 'lonja', 'Lj5A560T9' => 'lonja', 'Lj5C158T11' => 'lonja', 'Lj5C552T10' => 'lonja', 'Lj5C566G1' => 'lonja', 'Lj5C566G6' => 'lonja', 'Lj5g0018333' => 'lja', 'Lj6g0002626' => 'lja', 'Lj6g0024241' => 'lja', 'Lsat_1_v5_gn_2_64320' => 'lsa', 'Lsat_1_v5_gn_8_301' => 'lsa', 'Lsat_1_v5_gn_9_117041' => 'lsa', 'Manes.06G006100' => 'mes', 'Manes.07G031700' => 'mes', 'Manes.09G165600' => 'mes', 'Manes.14G171400' => 'mes', 'Mapoly0080s0043' => 'mpo', 'Mapoly0084s0044' => 'mpo', 'Mapoly0084s0045' => 'mpo', 'MBI05_g39043_MAGBIO' => 'mbi', 'MBI12_g33080_MAGBIO' => 'mbi', 'MBI19_g17587_MAGBIO' => 'mbi', 'MBI19_g17595_MAGBIO' => 'mbi', 'MCO02G388' => 'mco', 'MCO09G683' => 'mco', 'MD00G1147100' => 'mdo', 'MD00G1147200' => 'mdo', 'MD00G1192400' => 'mdo', 'MD00G1192500' => 'mdo', 'MD04G1207000' => 'mdo', 'MD05G1044300' => 'mdo', 'MD06G1227100' => 'mdo', 'MD10G1051400' => 'mdo', 'MD12G1220800' => 'mdo', 'MD12G1220900' => 'mdo', 'MD12G1221100' => 'mdo', 'MD12G1221300' => 'mdo', 'MD14G1236500' => 'mdo', 'Medtr1g082750' => 'mtr', 'Medtr4g094205' => 'mtr', 'Medtr4g126750' => 'mtr', 'Medtr8g107280' => 'mtr', 'MELO3C015328.2' => 'cme', 'MELO3C015329.2' => 'cme', 'MELO3C017360.2' => 'cme', 'MELO3C018637.2' => 'cme', 'Migut.B00605' => 'egut', 'Migut.D01540' => 'egut', 'Migut.F01717' => 'egut', 'Migut.N01072' => 'egut', 'MSTRG.4580' => 'ama', 'MSTRG.8132' => 'ama', 'MSTRG.9304' => 'ama', 'Nitab4.5_0000294g0010' => 'nta', 'Nitab4.5_0000327g0020' => 'nta', 'Nitab4.5_0002067g0060' => 'nta', 'Nitab4.5_0003401g0010' => 'nta', 'Nitab4.5_0004556g0020' => 'nta', 'Nitab4.5_0005818g0010' => 'nta', 'Nn3g18286' => 'nnu', 'Nn4g24242' => 'nnu', 'Nn4g26223' => 'nnu', 'Nn5g30089' => 'nnu', 'Oeu000249.3' => 'oeu', 'Oeu000793.1' => 'oeu', 'Oeu000798.1' => 'oeu', 'Oeu000804.1' => 'oeu', 'Oeu019231.2' => 'oeu', 'Oeu026279.1' => 'oeu', 'Oeu046164.2' => 'oeu', 'Os02g0754500' => 'osa', 'Os03g0707900' => 'osa', 'Os04g0117900' => 'osa', 'Os04g0118100' => 'osa', 'Peaxi162Scf00003g03540' => 'pax', 'Peaxi162Scf00003g03547' => 'pax', 'Peaxi162Scf00471g00004' => 'pax', 'Peaxi162Scf00683g00463' => 'pax', 'PGR083G0598' => 'pgr', 'PGR083G0653' => 'pgr', 'PGR083G1224' => 'pgr', 'PGR083G2513' => 'pgr', 'PGR142G1649' => 'pgr', 'PGSC0003DMG400005752' => 'stu', 'PGSC0003DMG400008518' => 'stu', 'PGSC0003DMG400016669' => 'stu', 'PGSC0003DMG400043451' => 'stu', 'Phvul.002G209800' => 'pvu', 'Phvul.002G330000' => 'pvu', 'Phvul.006G206200' => 'pvu', 'Phvul.007G180900' => 'pvu', 'Potri.001G205300' => 'ptr', 'Potri.012G046900' => 'ptr', 'Potri.013G024100' => 'ptr', 'Potri.013G024200' => 'ptr', 'Potri.015G038600' => 'ptr', 'Pp3c19_12600' => 'ppa', 'Pp3c20_10030' => 'ppa', 'Pp3c21_15880' => 'ppa', 'Pp3c21_15890' => 'ppa', 'Pp3c22_23080' => 'ppa', 'Pp3c7_6470' => 'ppa', 'PRCOL_00000136' => 'pco', 'PRCOL_00001088' => 'pco', 'Prupe.5G233600' => 'ppe', 'Prupe.6G327700' => 'ppe', 'Prupe.8G059900' => 'ppe', 'Psat4g001480' => 'psa', 'Psat6g149520' => 'psa', 'Psat7g099080' => 'psa', 'PSO017G1837' => 'pso', 'PSO170G0432' => 'pso', 'PSO170G5899' => 'pso', 'PSO478G3507' => 'pso', 'PSO541G2392' => 'pso', 'PSO781G0108' => 'pso', 'QL03p005842' => 'qlo', 'QL03p005872' => 'qlo', 'QL03p005878' => 'qlo', 'QL03p005900' => 'qlo', 'QL03p006454' => 'qlo', 'QL03p006470' => 'qlo', 'QL03p006480' => 'qlo', 'QL03p006495' => 'qlo', 'QL04p012585' => 'qlo', 'QL04p013580' => 'qlo', 'QL10p029608' => 'qlo', 'QL11p021330' => 'qlo', 'RcHm_v2.0_Chr3g0454411' => 'rch', 'RcHm_v2.0_Chr3g0454431' => 'rch', 'RcHm_v2.0_Chr3g0454461' => 'rch', 'RcHm_v2.0_Chr3g0454491' => 'rch', 'RcHm_v2.0_Chr7g0178361' => 'rch', 'Rhsim01G0080800' => 'rsi', 'Rhsim01G0085600' => 'rsi', 'Rhsim05G0106400' => 'rsi', 'Rhsim05G0143000' => 'rsi', 'Rhsim08G0126200' => 'rsi', 'Rhsim13G0168400' => 'rsi', 'RhsimUnG0207700' => 'rsi', 'Sabra01G0158200' => 'sbr', 'Sabra12G0032900' => 'sbr', 'Sabra13G0025700' => 'sbr', 'Sabra15G0037500' => 'sbr', 'SalBow1G1366' => 'sbo', 'SalBow5G0105' => 'sbo', 'SalBow6G6487' => 'sbo', 'Sc09g0003230' => 'sci', 'Sc12g0007230' => 'sci', 'Sc18g0006830' => 'sci', 'Sed0003731' => 'sed', 'Sed0010693' => 'sed', 'Sed0028182' => 'sed', 'SEGI_08361' => 'sgi', 'SEGI_16707' => 'sgi', 'SEGI_21767' => 'sgi', 'SEGI_22675' => 'sgi', 'SEGI_24729' => 'sgi', 'SEGI_27008' => 'sgi', 'SEGI_41595' => 'sgi', 'SGA_v2.0_scaffold172G39014' => 'sas', 'SGA_v2.0_scaffold2G01355' => 'sas', 'SGA_v2.0_scaffold36G14382' => 'sas', 'SGA_v2.0_scaffold45G17317' => 'sas', 'SHI19087' => 'shi', 'SMO338G0018' => 'smo', 'Solyc03g118690.4' => 'sly', 'Solyc10g047300.2' => 'sly', 'Solyc10g086170.1' => 'sly', 'Sopen03g037650' => 'spe', 'Sopen10g017560' => 'spe', 'Sopen10g035550' => 'spe', 'Sp1g07590' => 'spa', 'Sp1g35520' => 'spa', 'Sp3g16090' => 'spa', 'Sp6g33910' => 'spa', 'TAR374G1119' => 'tar', 'TAR622G0518' => 'tar', 'TAR622G0809' => 'tar', 'TAR622G1273' => 'tar', 'TAR628G1222' => 'tar', 'TAR633G0162' => 'tar', 'TAR633G1828' => 'tar', 'THA.LOC104799946' => 'tha', 'THA.LOC104820350' => 'tha', 'THA.LOC104820921' => 'tha', 'Thecc.02G138200' => 'tca', 'Thecc.03G056700' => 'tca', 'Thecc.05G305100' => 'tca', 'Thecc.05G305200' => 'tca', 'Thhalv10007679m.g' => 'esa', 'Thhalv10013019m.g' => 'esa', 'Thhalv10020361m.g' => 'esa', 'TPR.G1418' => 'tpr', 'TPR.G34521' => 'tpr', 'TPR.G6073' => 'tpr', 'TWI36G0290' => 'twi', 'TWI59G1224' => 'twi', 'TWI60G0055' => 'twi', 'TWI81G1069' => 'twi', 'unitig_27.g24923' => 'ugi', 'unitig_699.g19060' => 'ugi', 'unitig_8.g3412' => 'ugi', 'unitig_899.g15039' => 'ugi', 'vmacro17782' => 'vma', 'vmacro17783' => 'vma', 'vmacro19630' => 'vma', 'vmacro19937' => 'vma', 'VMungo0251G0933' => 'vmu', 'VMungo0251G3511' => 'vmu', 'VMungo0331G0265' => 'vmu', 'VMungo0540G1955' => 'vmu', 'VMungo0720G0875' => 'vmu', 'Zm00001eb054500' => 'zma', 'Zm00001eb109510' => 'zma', 'Zm00001eb216600' => 'zma', 'Zm00001eb255310' => 'zma' ) $gf_id = 'HOM05D001310' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001310' ) $data_identifier = 'HOM05D001310' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 15, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 10, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 8, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 13, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 7, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb255310' $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